The findings will undermine claims by the biotechnology industry that GM technology can boost food production without necessarily damaging the environment with pesticides.
Scientists from Cornell University in Ithaca, New York, carried out the study which involved interviews with hundreds of Chinese farmers who had switched to cotton that had been genetically modified with a gene for a bacterial toxin.
The toxin – known as Bt – is secreted by the GM cotton plant and is highly effective at stopping the growth of bollworm, a major pest of the crop that can cause millions of pounds worth of damage.
Major cotton producers, the United States, China, India and Argentina, quickly adopted Bt cotton after it was introduced in 1996 by Monsanto, the American biotechnology company.
Today, more than a third of the global cultivation of cotton is accounted for by Bt cotton, ranging from 42.8 million hectares in the United States to 3.7 million hectares in China.
Before the introduction of the GM crop into China, farmers in the country had to spray on average 20 times each growing season to control bollworm but, with Bt cotton, the average number of treatments fell to below seven.
The amount of pesticide also fell by 43.3kg per hectare in 1999, which was a decrease of about 71 per cent on previous years.
However, Professor Per Pinstrup-Andersen and his colleagues at Cornell found that all those benefits have since been largely lost due to the rise of other pests that were not considered a problem for cotton.
"Using a household survey from 2004, seven years after the initial commercialisation of Bt cotton in China, we show that total pesticide expenditure for Bt cotton farmers in China is nearly equal to that of their conventional counterparts," the scientists say in their report.
"Bt farmers in 2004 on the average have to spray pesticide 18.22 times, which is more than three times higher compared with 1999.
"Detailed information on pesticide expenditures reveals that, though Bt farmers saved 46 per cent of bollworm pesticide relative to non-Bt farmers, they spend 40 per cent more on pesticides designed to kill an emerging secondary pest," they say.
Secondary pests, such as a type of leaf bug called mirids, are not normally a problem in cotton fields because bollworm, and sprays against bollworm, tend to keep them in check.
However, because Bt cotton is targeted mainly against bollworm, other pests are able to exploit the relatively low use of pesticide that such fields need.
"These results should send a very strong signal to researchers and governments that they need to come up with remedial actions for the Bt-cotton farmers, otherwise these farmers will stop using Bt cotton and that would be very unfortunate," Professor Pinstrup-Andersen said.